Aptamers are single-strand DNA or RNA molecules that can be designed and produced rapidly and inexpensively to bind with high affinity and specificity to a desired target molecule. Proteins, peptides, and small molecules are all suitable targets. Aptamers can assume a variety of shapes. Because of their versatility, aptamers have a vast array of applications which include but are not limited to use as sensors, therapeutic tools, and cellular process regulators, as well as to guide drugs to their specific cellular targets. Aptamers are generally a good substitute for applications requiring an antibody because aptamers can be designed and produced rapidly, inexpensively, and most importantly, in vitro. DNA aptamers are stable for long periods without the strict storage requirements of antibodies. Perhaps most importantly as compared to antibodies, once identified, aptamers can be produced by purely synthetic means; that is, no organisms, cell culture or biological expression system is required. As such, unlike antibodies, aptamers reagents experience virtually no lot-to-lot variability. Further, facile modifications can be made to aptamers during synthesis that can confer nuclease stability of the molecules in serum for in vivo and diagnostic applications.
Characterization of the interaction between aptamers and their target molecules is of interest to the scientific community, because these interactions have broad applications ranging from drug delivery to metabolite detection. Two common methods of measuring binding affinity are surface plasmon resonance (SPR) and biolayer interferometry (BLI). SPR measures the localized change in the refractive index (RI) near the surface of a substrate in order to detect binding and has been used in a multiplex format. However, SPR is a heterogeneous method that requires complicated surface chemistry, immobilization, possible modification of one of the species being examined, and expensive gold-plated slides. Biolayer interferometry is a label-free technology for measuring biomolecular interactions. It is an optical analytical technique that analyzes the interference pattern of white light reflected from two surfaces: a layer of immobilized protein on the biosensor tip, and an internal reference layer. However, BLI also relies on surface immobilization and suffers from similar problems to SPR.